Use of a randomized sequence is especially important when evaluating
results of alignments (usually results of database searches) giving
weak homologies. In such cases is "good practice" to
perform subsequently a second search, but using a randomized version
of the sequence and then compare the results obtained in the two
runs.

Mode of operation

This program uses 2 windows: the top one should be filled from
the user, with a sequence of interest, while the other window
contains the result of the randomization. The following steps
must be performed:

Sequence input

Symbols used
Either paste or type in the top area the sequence of interest.
Any character or symbol that does not belong to the [a-zA-Z] set
is ignored.

removal of header information
Only the sequence must be placed in the top window: heading comments
must be removed

long sequences and small window
In order to allow users with small screens to still be able of
using this program, the size of each window had been made rather
small. Therefore, use the scroll-bars in order to move around
in the input and output windows. The suggested strategy is to
double click in the specified area and then do copy/paste from/to
the text-editor of choice or across different applications.

Case sensitivity choice
Often is useful to mark regions of interest by changing the Case.
This applet is capable of keeping those modifications also in
its output, as well as to change the case of the sequence according
to your wish. Therefore, by selecting any one of the 3 choices
provided, and hereafter described, the user has control on this
aspect. In order to choose the case in the output, the following
selections are possible, by clicking on the button close to them:

Unchanged, leaves the same case in the output as in
the input, and is useful if one wants to easier identify already
marked regions of the sequence

Shuffle
Once the sequence is placed in the top window, by pressing the
"SHUFFLE" button then the conversion is performed.

How to understand its output

Since both aim and mode of operation are rather straightforward,
also the understanding and the use of the results from this work
should not present any major difficulty. In fact, the output will
consist of simply a sequence with the same composition as the
input but in a fully unpredictable order.